The Uncanny Accuracy of Predictions From Virologists Manipulating Viruses in the Laboratory

From Fauci's boasts to research that pinpoints the directed evolution of furin cleavage sites to the same clade of viruses where SARS-CoV-2 falls, the number of coincidences is remarkable.

“Coincidence is the word we use when we can't see the levers and pulleys.” Sci-Fi Author Emma Bull

Here are four predictions that point to SARS-CoV-2 as an inevitable consequence of gain-of-function research.

PREDICTION 1. There will be a major outbreak during the Trump administration (Fauci):

Fauci said the following during his "Pandemic Preparedness in the Next Administration" speech, which came shortly before Trump's inauguration on Jan. 20.

"There is no question that there will be a challenge to the coming administration in the arena of infectious diseases.” He also said: "the thing we're extraordinarily confident about is that we're going to see this in the next few years."

PREDICTION 2. It will be a Coronavirus that infects ACE2 receptors:

“The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV underscores the threat of cross-species transmission events leading to outbreaks in humans. Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations¹. Using the SARS-CoV reverse genetics system², we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis. Evaluation of available SARS-based immune-therapeutic and prophylactic modalities revealed poor efficacy; both monoclonal antibody and vaccine approaches failed to neutralize and protect from infection with CoVs using the novel spike protein. On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations.”

PREDICTION 3. We’ll use this method, among others:

“Emergent and preemergent coronaviruses (CoVs) pose a global threat that requires immediate intervention. Rapid intervention necessitates the capacity to generate, grow, and genetically manipulate infectious CoVs in order to rapidly evaluate pathogenic mechanisms, host and tissue permissibility, and candidate antiviral therapeutic efficacy. CoVs encode the largest viral RNA genomes at about 28-32,000 nucleotides in length, and thereby complicate efficient engineering of the genome. Deconstructing the genome into manageable fragments affords the plasticity necessary to rapidly introduce targeted genetic changes in parallel and assort mutated fragments while maximizing genome stability over time. In this protocol we describe a well-developed reverse genetic platform strategy for CoVs that is comprised of partitioning the viral genome into 5-7 independent DNA fragments (depending on the CoV genome), each subcloned into a plasmid for increased stability and ease of genetic manipulation and amplification. Coronavirus genomes are conveniently partitioned by introducing type IIS or IIG restriction enzyme recognition sites that confer directional cloning. Since each restriction site leaves a unique overhang between adjoining fragments, reconstruction of the full-length genome can be achieved through a standard DNA ligation comprised of equal molar ratios of each fragment. Using this method, recombinant CoVs can be rapidly generated and used to investigate host range, gene function, pathogenesis, and candidate therapeutics for emerging and preemergent CoVs both in vitro and in vivo.”

PREDICTION 4. It will have a Furin Cleavage Site: Project DEFUSE Grant Proposal (Courtesy: The Intercept)

From: Efficient Reverse Genetic Systems for Rapid Genetic Manipulation of Emergent and Preemergent Infectious Coronaviruses

“RGD deletions: Small deletions at specific sites in the SARS-CoV RBD alter risk of human infection. We will analyze the functional consequences of these RBD deletions on SAR-CoV hACE-receptor usage, growth in HAE cultures and in vivo pathogenesis. First we will delete these regions, sequentially and in combination, in SHCO14 and SARS-Cov Urban, anticipating that the introduction of deletions will prevent virus growth in Vero cells and HAE, in parallel, we will evaluate whether RBD deletion repair restores the ability of low is strains to use human ACE2 and grow in human cells. 52Proteolytic Cleavage and Glycosylation Sites: After receptor binding, a variety of cell surface or endosomal proteases" cleave the SARS- CoV S glycoprotein causing massive changes in S structure" and activating fusion-mediated entry. We will analyze all SARS-CoV S gene sequences for appropriately conserved proteolytic cleavage sites in 52 and for the presence of potential furin cleavage sites. SARS-CoV with mismatches in proteolytic cleavage sites can be activated by exogenous trypsin or cathepsin L. Where clear mismatches occur, we will introduce appropriate human-specific cleavage sites and evaluate growth potential in Vero cell and HAE cultures. In SARS Cov, we will ablate several of these sites based on pseudotyped particle studies and evaluate the impact of select SARS CoV S changes on virus replication and pathogenesis. We will also review deep sequence data for low-abundant high-risk SARS-CoV that encode functional proteolytic cleavage sites, and if so, introduce these changes into the appropriate high-abundant, low-risk parental strain. N-Linked glycosylation: Some glycosylation events regulate SARS-CoV particle binding DC-SIGN/L-SIGN, alternative receptors for SARS-CoV entry into macrophages or monocytes”. Mutations that introduced two new N-linked glycosylation sites may have been involved in the emergence of human SARS-CoV from civet and raccoon dogs”. While the sites are absent from civet and raccoon dog strains and clade-2 SARS-CoV, they are present in WIVL, WIV36, and SHCO14, supporting a potential role of these sites in host jumping. To evaluate this, we will sequentially introduce clade 2 disrupting residues of SARS-CoV and SHCOL4 and evaluate virus growth in Vero cells nonpermissive cells ectopically expressing DC-SIGN, and in Human monocytes and macrophages anticipating reduced virus growth efficiency. We will introduce the clade 1 mutations that result in N-linked glycosylation in rs4237 RBD deletion repaired strains, evaluating virus growth efficiency in HAE, Vero cells, or nonpermissive cells +/- ectopic DC-SIGN expression. In vivo, we will evaluate pathogenesis in transgenic hACE2 mice.”

The leaked proposal can be found here.

Source of the DARPA Proposal: The Intercept 9/23/2021

“We will introduce appropriate human-specific cleavage sites and evaluate growth potential in [a type of mammalian cell commonly used in microbiology] and HAE cultures”

I did not forget Bill Gate’s predictions. He’s not a scientist, so I left him out.